I don’t seem to have the same disdain for the word ‘emergent’ as much of the population here. I don’t use it as a curiosity stopper or in place of the word ‘mysterious’ - I wouldn’t be much of a biologist if a little emergent behavior stopped me cold. (Also no argument about many modular things in biological systems, I pull out and manipulate pathways and regulatory circuits regularly in my work, but there is a whole lot which is still very context-dependent). In this context I used the word emergent to mean that rather than having some kind of map of the final structure embedded in the genetic instructions, you have them specifying the properties of small elements which then produce those larger structures only in the context of their interactions with each other and which produce a lot more structure than is actually encoded in the DNA via the rather-opaque ‘decompression algorithm’ of physics and chemistry (through which small simple changes to the elements can map to almost no change in the product or vast changes across multiple attributes). I’ve always found the analogy of genetics to a blueprint or algorithm tiresome and the analogy to a food recipe much more applicable; nothing in a recipe dictates things like, say, fluffyness other than the interactions of everything you put in in the context of an oven. You can alter biological systems in numerous ways with some regularity but only in some cases are there simple knobs you can turn to alter isolated attributes.
I mostly agree with your last two paragraphs, actually. Synthetic systems with properties similar to things like RNA or protein chemistry may eventually have a lot of power especially if they contain chemical properties not present in any of the basic building blocks of biology. They just will not have atomic-scale precision or arbitrary control over matter, and will be limited by things analogous to nutrients and metabolisms and either require a hell of a lot of functionality not directly connected to their main functions to hold themselves together or a lot of external infrastructure to make disposable things.
I really like your recipe analogy, I think it would be very useful for teaching molecular biology.
I think our discussion mirrors the tension between traditional biology and bioengineering. As a bioengineer I’m primarily concerned with what is possible to build given the biology we already know.
While I agree that a “blueprint” isn’t a good analogy for naturally evolved living organisms, this doesn’t prevent us from engineering new molecular systems that are built from a blueprint. As I mentioned, we already have turing complete molecular computers- and software compilers that can turn any code into a set of molecules that will perform the computation. It’s currently too slow and expensive to be useful, but it shows that programmable molecular systems are possible.
I don’t seem to have the same disdain for the word ‘emergent’ as much of the population here. I don’t use it as a curiosity stopper or in place of the word ‘mysterious’ - I wouldn’t be much of a biologist if a little emergent behavior stopped me cold. (Also no argument about many modular things in biological systems, I pull out and manipulate pathways and regulatory circuits regularly in my work, but there is a whole lot which is still very context-dependent). In this context I used the word emergent to mean that rather than having some kind of map of the final structure embedded in the genetic instructions, you have them specifying the properties of small elements which then produce those larger structures only in the context of their interactions with each other and which produce a lot more structure than is actually encoded in the DNA via the rather-opaque ‘decompression algorithm’ of physics and chemistry (through which small simple changes to the elements can map to almost no change in the product or vast changes across multiple attributes). I’ve always found the analogy of genetics to a blueprint or algorithm tiresome and the analogy to a food recipe much more applicable; nothing in a recipe dictates things like, say, fluffyness other than the interactions of everything you put in in the context of an oven. You can alter biological systems in numerous ways with some regularity but only in some cases are there simple knobs you can turn to alter isolated attributes.
I mostly agree with your last two paragraphs, actually. Synthetic systems with properties similar to things like RNA or protein chemistry may eventually have a lot of power especially if they contain chemical properties not present in any of the basic building blocks of biology. They just will not have atomic-scale precision or arbitrary control over matter, and will be limited by things analogous to nutrients and metabolisms and either require a hell of a lot of functionality not directly connected to their main functions to hold themselves together or a lot of external infrastructure to make disposable things.
I really like your recipe analogy, I think it would be very useful for teaching molecular biology.
I think our discussion mirrors the tension between traditional biology and bioengineering. As a bioengineer I’m primarily concerned with what is possible to build given the biology we already know.
While I agree that a “blueprint” isn’t a good analogy for naturally evolved living organisms, this doesn’t prevent us from engineering new molecular systems that are built from a blueprint. As I mentioned, we already have turing complete molecular computers- and software compilers that can turn any code into a set of molecules that will perform the computation. It’s currently too slow and expensive to be useful, but it shows that programmable molecular systems are possible.
It’s the usual analogy I see.